# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 12:56:50 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@@H]4O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 AYU  AYU  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate'  ligand  65  40  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AYU
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 AYU  N01  N  NH2    0  -0.817  -6.2061   4.1357  -2.5014
 AYU  C02  C  CR6    0   0.460  -6.3812   3.3606  -1.4309
 AYU  N03  N  N      0  -0.475  -7.2290   3.7507  -0.4720
 AYU  C04  C  CR16   0   0.046  -7.4003   2.9761   0.5958
 AYU  N05  N  N      0  -0.457  -6.8312   1.8146   0.8681
 AYU  C06  C  CR56   0   0.491  -5.9910   1.4407  -0.0936
 AYU  C07  C  CR56   0  -0.012  -5.7077   2.1377  -1.2572
 AYU  N08  N  N      0  -0.449  -4.7871   1.4630  -2.0179
 AYU  C09  C  CR15   0   0.112  -4.5272   0.3898  -1.3337
 AYU  N10  N  NR5    0  -0.539  -5.2261   0.3111  -0.1587
 AYU  C11  C  CH1    0   0.212  -5.1461  -0.7287   0.8348
 AYU  O12  O  O2     0  -0.490  -3.8160  -0.8799   1.2418
 AYU  C13  C  CH1    0  -0.037  -3.4847  -2.2656   1.3860
 AYU  C14  C  CH2    0  -0.153  -2.4778  -2.6909   0.3364
 AYU  O15  O  O2     0  -0.616  -1.3397  -1.8644   0.4205
 AYU  P16  P  P      0   1.338   0.1214  -2.5959   0.1926
 AYU  O17  O  O      0  -0.799   0.1794  -3.1786  -1.1843
 AYU  O18  O  OP    -1  -0.788   0.4334  -3.4362   1.3899
 AYU  O19  O  O2     0  -0.734   0.9513  -1.1799   0.2537
 AYU  P20  P  P      0   1.350   2.4349  -0.9991  -0.4292
 AYU  O21  O  OP    -1  -0.777   3.2493  -2.2248  -0.1824
 AYU  O22  O  O      0  -0.786   2.3095  -0.4021  -1.7930
 AYU  O23  O  O2     0  -0.638   2.8754   0.2089   0.6322
 AYU  C24  C  CH1    0   0.299   3.8231   1.1293   0.2280
 AYU  O25  O  O2     0  -0.501   5.0504   0.4568   0.1356
 AYU  C26  C  CH1    0  -0.011   6.1084   1.2622  -0.3294
 AYU  C27  C  CH1    0  -0.025   7.3156   0.3456  -0.5088
 AYU  O28  O  OH1    0  -0.664   7.7700  -0.1821   0.7155
 AYU  C29  C  CH2    0  -0.159   7.0014  -0.7473  -1.5228
 AYU  O30  O  OH1    0  -0.673   8.1894  -1.4513  -1.8034
 AYU  C31  C  CH1    0   0.051   6.3442   2.4188   0.6421
 AYU  O32  O  OH1    0  -0.679   7.3451   3.2406   0.0915
 AYU  C33  C  CH1    0  -0.005   5.0367   3.1855   0.8268
 AYU  O34  O  OH1    0  -0.672   5.2746   4.2180   1.7536
 AYU  C35  C  CH1    0  -0.040   3.9073   2.2535   1.2574
 AYU  O36  O  OH1    0  -0.668   4.1776   1.7726   2.5468
 AYU  C37  C  CH1    0  -0.032  -4.8017  -3.0219   1.2689
 AYU  O38  O  OH1    0  -0.668  -5.4022  -3.0785   2.5369
 AYU  C39  C  CH1    0  -0.051  -5.5884  -2.1025   0.3327
 AYU  O40  O  OH1    0  -0.654  -6.9767  -2.2160   0.4172
 AYU  H1   H  HNH2   0   0.412  -5.5867   3.8659  -3.2450
 AYU  H2   H  HNH2   0   0.404  -6.7096   5.0013  -2.5881
 AYU  H3   H  HCR6   0   0.252  -8.0989   3.3513   1.3362
 AYU  H4   H  HCR5   0   0.295  -3.8274  -0.3771  -1.6313
 AYU  H5   H  HCH1   0   0.261  -5.7885  -0.4058   1.6617
 AYU  H6   H  HCH1   0   0.260  -3.0427  -2.4120   2.3761
 AYU  H7   H  HCH2   0   0.225  -2.2462  -3.7466   0.5198
 AYU  H8   H  HCH2   0   0.212  -2.9097  -2.6327  -0.6706
 AYU  H11  H  HCH1   0   0.194   3.5686   1.5628  -0.7530
 AYU  H12  H  HCH1   0   0.220   5.8581   1.6903  -1.3148
 AYU  H13  H  HCH1   0   0.244   8.1361   0.9513  -0.9041
 AYU  H14  H  HOH1   0   0.442   7.0511  -0.6893   1.1089
 AYU  H15  H  HCH2   0   0.208   6.2217  -1.4087  -1.1239
 AYU  H16  H  HCH2   0   0.193   6.5880  -0.2774  -2.4262
 AYU  H17  H  HOH1   0   0.454   7.9634  -2.2101  -2.3479
 AYU  H18  H  HCH1   0   0.212   6.6558   2.0101   1.6128
 AYU  H19  H  HOH1   0   0.451   7.4643   3.9939   0.6789
 AYU  H20  H  HCH1   0   0.222   4.7541   3.6014  -0.1520
 AYU  H21  H  HOH1   0   0.456   4.5998   4.8945   1.6431
 AYU  H22  H  HCH1   0   0.224   2.9578   2.8114   1.2271
 AYU  H23  H  HOH1   0   0.450   3.5119   1.1121   2.7657
 AYU  H24  H  HCH1   0   0.253  -4.6637  -4.0232   0.8399
 AYU  H25  H  HOH1   0   0.449  -6.3430  -3.2499   2.4126
 AYU  H26  H  HCH1   0   0.250  -5.2331  -2.2541  -0.6949
 AYU  H27  H  HOH1   0   0.470  -7.2649  -2.9334  -0.1561

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 AYU  O36  C35  single    1.402  0.020  1.402
 AYU  O34  C33  single    1.408  0.020  1.408
 AYU  C35  C33  single    1.526  0.020  1.526
 AYU  C35  C24  single    1.527  0.020  1.527
 AYU  O22  P20  deloc     1.494  0.020  1.494
 AYU  O23  C24  single    1.381  0.020  1.381
 AYU  O23  P20  single    1.667  0.020  1.667
 AYU  O17  P16  deloc     1.496  0.020  1.496
 AYU  C33  C31  single    1.527  0.020  1.527
 AYU  C24  O25  single    1.403  0.020  1.403
 AYU  P20  O21  deloc     1.492  0.020  1.492
 AYU  P20  O19  single    1.643  0.020  1.643
 AYU  N01  C02  single    1.333  0.020  1.333
 AYU  C31  O32  single    1.407  0.020  1.407
 AYU  C31  C26  single    1.529  0.020  1.529
 AYU  O18  P16  deloc     1.496  0.020  1.496
 AYU  P16  O19  single    1.642  0.020  1.642
 AYU  P16  O15  single    1.650  0.020  1.650
 AYU  N08  C09  aromatic  1.299  0.020  1.299
 AYU  N08  C07  aromatic  1.372  0.020  1.372
 AYU  O25  C26  single    1.409  0.020  1.409
 AYU  C09  N10  aromatic  1.369  0.020  1.369
 AYU  C02  C07  aromatic  1.407  0.020  1.407
 AYU  C02  N03  aromatic  1.338  0.020  1.338
 AYU  C07  C06  aromatic  1.386  0.020  1.386
 AYU  C26  C27  single    1.526  0.020  1.526
 AYU  O28  C27  single    1.408  0.020  1.408
 AYU  O40  C39  single    1.395  0.020  1.395
 AYU  O15  C14  single    1.409  0.020  1.409
 AYU  C39  C37  single    1.530  0.020  1.530
 AYU  C39  C11  single    1.528  0.020  1.528
 AYU  N03  C04  aromatic  1.330  0.020  1.330
 AYU  N10  C06  aromatic  1.366  0.020  1.366
 AYU  N10  C11  single    1.440  0.020  1.440
 AYU  C27  C29  single    1.524  0.020  1.524
 AYU  C06  N05  aromatic  1.331  0.020  1.331
 AYU  C37  C13  single    1.523  0.020  1.523
 AYU  C37  O38  single    1.404  0.020  1.404
 AYU  C11  O12  single    1.399  0.020  1.399
 AYU  C04  N05  aromatic  1.322  0.020  1.322
 AYU  C29  O30  single    1.409  0.020  1.409
 AYU  C14  C13  single    1.515  0.020  1.515
 AYU  O12  C13  single    1.432  0.020  1.432
 AYU  N01  H1   single    0.860  0.020  1.020
 AYU  N01  H2   single    0.860  0.020  1.020
 AYU  C04  H3   single    0.930  0.020  1.080
 AYU  C09  H4   single    0.930  0.020  1.080
 AYU  C11  H5   single    0.970  0.020  1.090
 AYU  C13  H6   single    0.970  0.020  1.090
 AYU  C14  H7   single    0.970  0.020  1.090
 AYU  C14  H8   single    0.970  0.020  1.090
 AYU  C24  H11  single    0.970  0.020  1.090
 AYU  C26  H12  single    0.970  0.020  1.090
 AYU  C27  H13  single    0.970  0.020  1.090
 AYU  O28  H14  single    0.850  0.020  0.980
 AYU  C29  H15  single    0.970  0.020  1.090
 AYU  C29  H16  single    0.970  0.020  1.090
 AYU  O30  H17  single    0.850  0.020  0.980
 AYU  C31  H18  single    0.970  0.020  1.090
 AYU  O32  H19  single    0.850  0.020  0.980
 AYU  C33  H20  single    0.970  0.020  1.090
 AYU  O34  H21  single    0.850  0.020  0.980
 AYU  C35  H22  single    0.970  0.020  1.090
 AYU  O36  H23  single    0.850  0.020  0.980
 AYU  C37  H24  single    0.970  0.020  1.090
 AYU  O38  H25  single    0.850  0.020  0.980
 AYU  C39  H26  single    0.970  0.020  1.090
 AYU  O40  H27  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 AYU  H2   N01  H1   118.44  3.000
 AYU  H2   N01  C02  120.27  3.000
 AYU  H1   N01  C02  121.28  3.000
 AYU  C07  C02  N03  117.92  3.000
 AYU  N03  C02  N01  119.29  3.000
 AYU  C07  C02  N01  122.79  3.000
 AYU  C04  N03  C02  119.15  3.000
 AYU  H3   C04  N05  116.13  3.000
 AYU  H3   C04  N03  115.43  3.000
 AYU  N05  C04  N03  128.44  3.000
 AYU  C06  N05  C04  111.71  3.000
 AYU  N10  C06  C07  105.16  3.000
 AYU  N10  C06  N05  128.35  3.000
 AYU  C07  C06  N05  126.49  3.000
 AYU  N08  C07  C06  110.82  3.000
 AYU  C06  C07  C02  116.30  3.000
 AYU  N08  C07  C02  132.87  3.000
 AYU  C09  N08  C07  104.39  3.000
 AYU  H4   C09  N10  121.75  3.000
 AYU  H4   C09  N08  124.83  3.000
 AYU  N10  C09  N08  113.41  3.000
 AYU  C11  N10  C09  127.23  3.000
 AYU  C11  N10  C06  126.53  3.000
 AYU  C09  N10  C06  106.21  3.000
 AYU  H5   C11  C39  110.07  3.000
 AYU  H5   C11  O12  111.69  3.000
 AYU  C39  C11  O12  105.88  3.000
 AYU  H5   C11  N10  105.98  3.000
 AYU  O12  C11  N10  109.36  3.000
 AYU  C39  C11  N10  113.97  3.000
 AYU  C13  O12  C11  110.72  3.000
 AYU  H6   C13  C37  110.63  3.000
 AYU  H6   C13  C14  108.71  3.000
 AYU  C37  C13  C14  112.45  3.000
 AYU  H6   C13  O12  108.30  3.000
 AYU  C14  C13  O12  110.83  3.000
 AYU  C37  C13  O12  105.82  3.000
 AYU  H8   C14  H7   106.73  3.000
 AYU  H8   C14  O15  109.98  3.000
 AYU  H7   C14  O15  112.60  3.000
 AYU  H8   C14  C13  111.05  3.000
 AYU  H7   C14  C13  107.14  3.000
 AYU  O15  C14  C13  109.31  3.000
 AYU  P16  O15  C14  116.55  3.000
 AYU  O19  P16  O18  110.44  3.000
 AYU  O19  P16  O17  110.51  3.000
 AYU  O18  P16  O17  120.65  3.000
 AYU  O19  P16  O15   93.45  3.000
 AYU  O18  P16  O15  108.86  3.000
 AYU  O17  P16  O15  109.52  3.000
 AYU  P20  O19  P16  122.39  3.000
 AYU  O23  P20  O22  108.29  3.000
 AYU  O23  P20  O21  110.22  3.000
 AYU  O22  P20  O21  121.67  3.000
 AYU  O21  P20  O19  109.49  3.000
 AYU  O23  P20  O19   93.08  3.000
 AYU  O22  P20  O19  110.34  3.000
 AYU  C24  O23  P20  118.53  3.000
 AYU  H11  C24  C35  108.86  3.000
 AYU  H11  C24  O25  109.39  3.000
 AYU  C35  C24  O25  110.44  3.000
 AYU  H11  C24  O23  111.35  3.000
 AYU  O25  C24  O23  107.46  3.000
 AYU  C35  C24  O23  109.34  3.000
 AYU  C26  O25  C24  113.88  3.000
 AYU  H12  C26  C31  108.00  3.000
 AYU  H12  C26  C27  107.91  3.000
 AYU  C31  C26  C27  114.02  3.000
 AYU  H12  C26  O25  110.26  3.000
 AYU  C27  C26  O25  106.83  3.000
 AYU  C31  C26  O25  109.79  3.000
 AYU  H13  C27  C29  108.14  3.000
 AYU  H13  C27  O28  106.24  3.000
 AYU  C29  C27  O28  112.10  3.000
 AYU  H13  C27  C26  107.65  3.000
 AYU  C29  C27  C26  110.23  3.000
 AYU  O28  C27  C26  112.21  3.000
 AYU  H14  O28  C27  108.15  3.000
 AYU  H16  C29  H15  106.82  3.000
 AYU  H16  C29  O30  111.53  3.000
 AYU  H15  C29  O30  111.73  3.000
 AYU  H16  C29  C27  108.54  3.000
 AYU  H15  C29  C27  109.69  3.000
 AYU  O30  C29  C27  108.48  3.000
 AYU  H17  O30  C29  108.00  3.000
 AYU  H18  C31  C33  108.84  3.000
 AYU  H18  C31  O32  111.18  3.000
 AYU  C33  C31  O32  111.29  3.000
 AYU  H18  C31  C26  108.90  3.000
 AYU  O32  C31  C26  107.63  3.000
 AYU  C33  C31  C26  108.94  3.000
 AYU  H19  O32  C31  107.84  3.000
 AYU  H20  C33  C35  106.96  3.000
 AYU  H20  C33  O34  110.60  3.000
 AYU  C35  C33  O34  112.78  3.000
 AYU  H20  C33  C31  107.59  3.000
 AYU  C35  C33  C31  111.17  3.000
 AYU  O34  C33  C31  107.65  3.000
 AYU  H21  O34  C33  108.76  3.000
 AYU  H22  C35  O36  111.41  3.000
 AYU  H22  C35  C33  108.71  3.000
 AYU  O36  C35  C33  109.03  3.000
 AYU  H22  C35  C24  107.87  3.000
 AYU  C33  C35  C24  107.47  3.000
 AYU  O36  C35  C24  112.21  3.000
 AYU  H23  O36  C35  108.12  3.000
 AYU  H24  C37  C39  111.93  3.000
 AYU  H24  C37  O38  111.71  3.000
 AYU  C39  C37  O38  110.91  3.000
 AYU  H24  C37  C13  111.97  3.000
 AYU  O38  C37  C13  108.69  3.000
 AYU  C39  C37  C13  101.14  3.000
 AYU  H25  O38  C37  107.94  3.000
 AYU  H26  C39  O40  111.56  3.000
 AYU  H26  C39  C37  108.87  3.000
 AYU  O40  C39  C37  115.19  3.000
 AYU  H26  C39  C11  109.76  3.000
 AYU  C37  C39  C11  100.97  3.000
 AYU  O40  C39  C11  109.95  3.000
 AYU  H27  O40  C39  108.81  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 AYU  CONST_01  C09  N08  C07  C02  180.00   0.0  0
 AYU  CONST_02  N10  C06  C07  C02  180.00   0.0  0
 AYU  CONST_03  N05  C06  C07  C02    0.00   0.0  0
 AYU  CONST_04  N05  C04  N03  C02    0.00   0.0  0
 AYU  CONST_05  N08  C07  C02  N03  180.00   0.0  0
 AYU  CONST_06  C06  C07  C02  N03    0.00   0.0  0
 AYU  CONST_07  C06  N05  C04  N03    0.00   0.0  0
 AYU  CONST_08  C07  C02  N03  C04    0.00   0.0  0
 AYU  CONST_09  C07  C06  N05  C04    0.00   0.0  0
 AYU  CONST_10  N10  C06  N05  C04  180.00   0.0  0
 AYU  CONST_11  N08  C07  C06  N05  180.00   0.0  0
 AYU  CONST_12  C09  N10  C06  N05  180.00   0.0  0
 AYU  CONST_13  C09  N08  C07  C06    0.00   0.0  0
 AYU  CONST_14  N08  C09  N10  C06    0.00   0.0  0
 AYU  CONST_15  N10  C09  N08  C07    0.00   0.0  0
 AYU  CONST_16  C09  N10  C06  C07    0.00   0.0  0
 AYU  CONST_17  N10  C06  C07  N08    0.00   0.0  0
 AYU  CONST_18  C11  N10  C06  N05    0.00   0.0  0
 AYU  CONST_19  C11  N10  C06  C07  180.00   0.0  0
 AYU  CONST_20  C11  N10  C09  N08  180.00   0.0  0
 AYU  CONST_21  N08  C07  C02  N01    0.00   0.0  0
 AYU  CONST_22  C06  C07  C02  N01  180.00   0.0  0
 AYU  CONST_23  C04  N03  C02  N01  180.00   0.0  0
 AYU  CONST_24  H3   C04  N03  C02  180.00   0.0  0
 AYU  CONST_25  H4   C09  N10  C06  180.00   0.0  0
 AYU  CONST_26  H1   N01  C02  N03  180.00   0.0  0
 AYU  CONST_27  H2   N01  C02  N03    0.00   0.0  0
 AYU  Var_01    O17  P16  O15  C14   61.57  30.0  1
 AYU  Var_02    O22  P20  O19  P16   95.94  30.0  2
 AYU  Var_03    H7   C14  O15  P16   22.55  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 AYU  chir_01  C11  C39  N10  O12  positiv
 AYU  chir_02  C13  O12  C14  C37  positiv
 AYU  chir_05  C24  C35  O23  O25  positiv
 AYU  chir_06  C26  O25  C27  C31  positiv
 AYU  chir_07  C27  O28  C26  C29  positiv
 AYU  chir_08  C31  O32  C26  C33  positiv
 AYU  chir_09  C33  O34  C35  C31  positiv
 AYU  chir_10  C35  O36  C24  C33  positiv
 AYU  chir_11  C37  C39  C13  O38  negativ
 AYU  chir_12  C39  O40  C11  C37  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 AYU  plan-1  N01  0.020
 AYU  plan-1  C02  0.020
 AYU  plan-1  H1   0.020
 AYU  plan-1  H2   0.020
 AYU  plan-2  N01  0.020
 AYU  plan-2  C02  0.020
 AYU  plan-2  N03  0.020
 AYU  plan-2  C04  0.020
 AYU  plan-2  N05  0.020
 AYU  plan-2  C06  0.020
 AYU  plan-2  C07  0.020
 AYU  plan-2  N08  0.020
 AYU  plan-2  C09  0.020
 AYU  plan-2  N10  0.020
 AYU  plan-2  C11  0.020
 AYU  plan-2  H3   0.020
 AYU  plan-2  H4   0.020

